Error when install SCT

zmzforever · November 29, 2019, 2:21am

Neurodebian system with SCT v. 4.0.0.

Validate installation...


--
Spinal Cord Toolbox (dev)

SCT info:
- version: dev
- path: /home/brain/sct_dev
OS: linux (Linux-3.16.0-4-amd64-x86_64-with-debian-8.0)
CPU cores: Available: 1, Used by SCT: 1
RAM: MemTotal:        1851804 kB
total       used       free     shared    buffers     cached
Mem:          1808       1359        449          7         67       1054
-/+ buffers/cache:        237       1570
Swap:         1951          0       1951
Check Python executable.............................[OK]
  Using bundled python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) 
[GCC 7.3.0] at /home/brain/sct_dev/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.17.4)
Check if cryptography is installed..................[OK] (2.8)
Check if dipy is installed..........................[OK] (1.0.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras is installed.........................[OK] (2.3.1)
Check if matplotlib is installed....................[OK] (3.1.2)
Check if nibabel is installed.......................[OK] (2.5.1)
Check if pandas is installed........................[OK] (0.25.3)
Check if psutil is installed........................[OK] (5.6.7)
Check if pyqt5 (5.11.3) is installed................[OK]
Check if pytest is installed........................[OK] (5.3.1)
Check if pytest-cov is installed....................[OK] (2.8.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.3.3)
Check if scikit-image is installed..................[OK] (0.16.2)
Check if scikit-learn is installed..................[OK] (0.21.3)
Check if tensorflow is installed....................[OK] (2.0.0)
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.39.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.7)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if DISPLAY variable is set....................[OK]
Check if figure can be opened with PyQt.............libGL error: pci id for fd 12: 80ee:beef, driver (null)
OpenGL Warning: glFlushVertexArrayRangeNV not found in mesa table
OpenGL Warning: glVertexArrayRangeNV not found in mesa table
OpenGL Warning: glCombinerInputNV not found in mesa table
OpenGL Warning: glCombinerOutputNV not found in mesa table
OpenGL Warning: glCombinerParameterfNV not found in mesa table
OpenGL Warning: glCombinerParameterfvNV not found in mesa table
OpenGL Warning: glCombinerParameteriNV not found in mesa table
OpenGL Warning: glCombinerParameterivNV not found in mesa table
OpenGL Warning: glFinalCombinerInputNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterivNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glDeleteFencesNV not found in mesa table
OpenGL Warning: glFinishFenceNV not found in mesa table
OpenGL Warning: glGenFencesNV not found in mesa table
OpenGL Warning: glGetFenceivNV not found in mesa table
OpenGL Warning: glIsFenceNV not found in mesa table
OpenGL Warning: glSetFenceNV not found in mesa table
OpenGL Warning: glTestFenceNV not found in mesa table
libGL error: core dri or dri2 extension not found
libGL error: failed to load driver: vboxvideo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee910
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3cc0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3ea0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2efee0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f00c0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f5340
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f5520
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ef3a0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ef580
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4800
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f49e0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ef940
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2efb20
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4da0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4f80
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2eecd0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2eeeb0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4260
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4440
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2e9f50
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ec610
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f20a0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2280
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee190
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee370
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3720
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3900
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed650
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed830
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2be0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2dc0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2edbf0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2eddd0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3180
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3360
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed0b0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed290
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2640
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2820
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee820
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2eea00
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3db0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3f90
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2effd0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f01b0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f5430
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f5610
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ef490
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ef670
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f48f0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4ad0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2efa30
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2efc10
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4e90
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f5070
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2eedc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ef0d0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4350
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f4530
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ec520
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ecde0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2190
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2370
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee280
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee460
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3810
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f39f0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed740
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed920
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2cd0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2eb0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2edce0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2edec0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3270
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f3450
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed1a0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ed380
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2730
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2f2910
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f340f2ee730, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f340f2ee730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
Could not initialize GLX
./install_sct: line 658:  1564 Aborted                 sct_check_dependencies

Installation validation Failed!

Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):

http://forum.spinalcordmri.org/c/sct


Installation failed

jcohenadad · November 29, 2019, 2:47am

@zmzforever could you please try our latest version v4.1.1? We’ve fixed a few issues in sct_check_dependencies.
Cheers
Julien

zmzforever · November 29, 2019, 6:02pm

Have tried v4.1.1:

Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y


Validate installation...


--
Spinal Cord Toolbox (dev)

SCT info:
- version: dev
- path: /home/brain/sct_dev
OS: linux (Linux-3.16.0-4-amd64-x86_64-with-debian-8.0)
CPU cores: Available: 1, Used by SCT: 1
RAM: MemTotal:        1851804 kB
total       used       free     shared    buffers     cached
Mem:          1808       1454        353         40         56       1065
-/+ buffers/cache:        332       1476
Swap:         1951          1       1950
Check Python executable.............................[OK]
  Using bundled python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31) 
[GCC 7.3.0] at /home/brain/sct_dev/python/envs/venv_sct/bin/python
Check if data are installed.........................[OK]
Check if numpy is installed.........................[OK] (1.17.4)
Check if cryptography is installed..................[OK] (2.8)
Check if dipy is installed..........................[OK] (1.0.0)
Check if futures is installed.......................[OK]
Check if h5py is installed..........................[OK] (2.10.0)
Check if Keras is installed.........................[OK] (2.3.1)
Check if matplotlib is installed....................[OK] (3.1.2)
Check if nibabel is installed.......................[OK] (2.5.1)
Check if pandas is installed........................[OK] (0.25.3)
Check if psutil is installed........................[OK] (5.6.7)
Check if pyqt5 (5.11.3) is installed................[OK]
Check if pytest is installed........................[OK] (5.3.1)
Check if pytest-cov is installed....................[OK] (2.8.1)
Check if raven is installed.........................[OK]
Check if requests is installed......................[OK] (2.22.0)
Check if scipy is installed.........................[OK] (1.3.3)
Check if scikit-image is installed..................[OK] (0.16.2)
Check if scikit-learn is installed..................[OK] (0.21.3)
Check if tensorflow is installed....................[OK] (2.0.0)
Check if xlrd is installed..........................[OK] (1.2.0)
Check if xlutils is installed.......................[OK]
Check if xlwt is installed..........................[OK] (1.3.0)
Check if tqdm is installed..........................[OK] (4.39.0)
Check if transforms3d is installed..................[OK] (0.3.1)
Check if urllib3[secure] is installed...............[OK] (1.25.7)
Check if spinalcordtoolbox is installed.............[OK]
Check ANTs compatibility with OS ...................[OK]
Check PropSeg compatibility with OS ................[OK]
Check if DISPLAY variable is set....................[OK]
Check if figure can be opened with PyQt.............libGL error: pci id for fd 12: 80ee:beef, driver (null)
OpenGL Warning: glFlushVertexArrayRangeNV not found in mesa table
OpenGL Warning: glVertexArrayRangeNV not found in mesa table
OpenGL Warning: glCombinerInputNV not found in mesa table
OpenGL Warning: glCombinerOutputNV not found in mesa table
OpenGL Warning: glCombinerParameterfNV not found in mesa table
OpenGL Warning: glCombinerParameterfvNV not found in mesa table
OpenGL Warning: glCombinerParameteriNV not found in mesa table
OpenGL Warning: glCombinerParameterivNV not found in mesa table
OpenGL Warning: glFinalCombinerInputNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterivNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glDeleteFencesNV not found in mesa table
OpenGL Warning: glFinishFenceNV not found in mesa table
OpenGL Warning: glGenFencesNV not found in mesa table
OpenGL Warning: glGetFenceivNV not found in mesa table
OpenGL Warning: glIsFenceNV not found in mesa table
OpenGL Warning: glSetFenceNV not found in mesa table
OpenGL Warning: glTestFenceNV not found in mesa table
libGL error: core dri or dri2 extension not found
libGL error: failed to load driver: vboxvideo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7eea0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84250
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84430
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b80470
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b80650
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b858d0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b85ab0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7f930
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7fb10
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84d90
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84f70
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7fed0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b800b0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b85330
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b85510
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7f260
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7f440
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b847f0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b849d0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7a4e0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7cba0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82630
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82810
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e720
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e900
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83cb0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83e90
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7dbe0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ddc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83170
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83350
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e180
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e360
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83710
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b838f0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7d640
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7d820
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82bd0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82db0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7edb0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ef90
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84340
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84520
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b80560
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b80740
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b859c0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b85ba0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7fa20
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7fc00
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84e80
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b85060
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ffc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b801a0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b85420
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b85600
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7f350
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7f660
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b848e0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b84ac0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7cab0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7d370
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82720
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82900
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e810
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e9f0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83da0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83f80
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7dcd0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7deb0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83260
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83440
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e270
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7e450
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b83800
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b839e0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7d730
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7d910
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82cc0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b82ea0
OpenGL Warning: Retry with 0x8003 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
OpenGL Warning: glXGetFBConfigAttrib for 0x7f2687b7ecc0, failed to get XVisualInfo
OpenGL Warning: XGetVisualInfo returned 0 visuals for 0x7f2687b7ecc0
OpenGL Warning: Retry with 0x8002 returned 0 visuals
Could not initialize GLX
./install_sct: line 658:  1609 Aborted                 sct_check_dependencies

Installation validation Failed!

Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum (create a new discussion):

http://forum.spinalcordmri.org/c/sct


Installation failed

jcohenadad · November 29, 2019, 6:06pm

How do you run SCT? Locally or via a virtual machine or via Docker or via ssh? If via ssh, did you enable X forwarding?

zmzforever · December 1, 2019, 1:33am

Via Neurodebian. Docker didn’t work for me. So I installed Virtualbox and ran Neurodebian system.

zmzforever · December 2, 2019, 9:05am

Plus. I assumed there was something wrong with my virtual machine. So I switched to VM, it still didn’t work. Also, I tried Tecent Cloud, using Ubuntu. Here is the result:

To run a command as administrator (user "root"), use "sudo &lt;command&gt;".
See "man sudo_root" for details.

zmzforever@VM-0-14-ubuntu:~$ root

Command 'root' not found, did you mean:

  command 'roo' from snap roo (2.0.3)
  command 'toot' from snap toot (0.24.0)
  command 'proot' from deb proot
  command 'rott' from deb rott
  command 'rootv' from deb xawtv

See 'snap info &lt;snapname&gt;' for additional versions.

zmzforever@VM-0-14-ubuntu:~$ cd /home/zmzforever/Downloads/spinalcordtoolbox-master
zmzforever@VM-0-14-ubuntu:~/Downloads/spinalcordtoolbox-master$ ./install_sct

*******************************
* Welcome to SCT installation *
*******************************

Checking requirements...

SCT version ......... dev
Installation type ... package
Operating system .... linux
Shell config ........ /home/zmzforever/.bashrc

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: y

--&gt; Crash reports will be sent to the SCT development team. Thank you!

SCT will be installed here: [/home/zmzforever/sct_dev]

Do you agree? [y]es/[n]o: y

Copying source files from /home/zmzforever/Downloads/spinalcordtoolbox-master to /home/zmzforever/sct_dev

...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Installing conda...

rm -rf /home/zmzforever/sct_dev/python

mkdir -p /home/zmzforever/sct_dev/python

wget -O /tmp/tmp.mj4wXqC3dV/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2019-12-02 16:43:17--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c94f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.200.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 71785000 (68M) [application/x-sh]
Saving to: ‘/tmp/tmp.mj4wXqC3dV/miniconda.sh’

/tmp/tmp.mj4wXqC3dV 100%[===================&gt;]  68.46M  5.78MB/s    in 12s     

2019-12-02 16:43:30 (5.49 MB/s) - ‘/tmp/tmp.mj4wXqC3dV/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.mj4wXqC3dV/miniconda.sh -p /home/zmzforever/sct_dev/python -b -f

PREFIX=/home/zmzforever/sct_dev/python
Unpacking payload ...
Extracting : libedit-3.1.20181209-hc058e9b_0.conda:   3%| | 1/35 [00:00&lt;00:03,  Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda:   6%| | 2/35 [00:00&lt;00:03,  9.01iExtracting : libgcc-ng-9.1.0-hdf63c60_0.conda:   9%| | 3/35 [00:00&lt;00:03,  9.31iExtracting : urllib3-1.24.2-py37_0.conda:   9%|▏ | 3/35 [00:00&lt;00:03,  9.31it/s]Extracting : pyopenssl-19.0.0-py37_0.conda:  11%| | 4/35 [00:00&lt;00:03,  9.31it/sExtracting : six-1.12.0-py37_0.conda:  14%|▊     | 5/35 [00:00&lt;00:03,  9.31it/s]Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  20%|▏| 7/35 [00:00&lt;00:03,  9.Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  23%|▏| 8/35 [00:00&lt;00:02, 11.Extracting : python-3.7.4-h265db76_1.conda:  23%|▏| 8/35 [00:01&lt;00:02, 11.46it/sExtracting : libffi-3.2.1-hd88cf55_4.conda:  26%|▎| 9/35 [00:01&lt;00:02, 11.46it/sExtracting : libffi-3.2.1-hd88cf55_4.conda:  29%|▎| 10/35 [00:01&lt;00:05,  4.29it/Extracting : pycparser-2.19-py37_0.conda:  29%|▎| 10/35 [00:01&lt;00:05,  4.29it/s]Extracting : chardet-3.0.4-py37_1003.conda:  31%|▎| 11/35 [00:01&lt;00:05,  4.29it/Extracting : readline-7.0-h7b6447c_5.conda:  34%|▎| 12/35 [00:01&lt;00:05,  4.29it/Extracting : readline-7.0-h7b6447c_5.conda:  37%|▎| 13/35 [00:01&lt;00:03,  5.72it/Extracting : yaml-0.1.7-had09818_2.conda:  37%|▎| 13/35 [00:01&lt;00:03,  5.72it/s]Extracting : conda-package-handling-1.6.0-py37h7b6447c_0.conda:  40%|▍| 14/35 [0Extracting : pycosat-0.6.3-py37h14c3975_0.conda:  43%|▍| 15/35 [00:01&lt;00:03,  5.Extracting : pycosat-0.6.3-py37h14c3975_0.conda:  46%|▍| 16/35 [00:01&lt;00:02,  7.Extracting : tk-8.6.8-hbc83047_0.conda:  46%|█▎ | 16/35 [00:02&lt;00:02,  7.45it/s]Extracting : _libgcc_mutex-0.1-main.conda:  49%|▍| 17/35 [00:02&lt;00:02,  7.45it/sExtracting : _libgcc_mutex-0.1-main.conda:  51%|▌| 18/35 [00:02&lt;00:01,  8.52it/sExtracting : ncurses-6.1-he6710b0_1.conda:  51%|▌| 18/35 [00:02&lt;00:01,  8.52it/sExtracting : xz-5.2.4-h14c3975_4.conda:  54%|█▋ | 19/35 [00:02&lt;00:01,  8.52it/s]Extracting : ruamel_yaml-0.15.46-py37h14c3975_0.conda:  57%|▌| 20/35 [00:02&lt;00:0Extracting : tqdm-4.36.1-py_0.conda:  60%|███▌  | 21/35 [00:02&lt;00:01,  8.26it/s]Extracting : certifi-2019.9.11-py37_0.tar.bz2:  66%|▋| 23/35 [00:02&lt;00:01, 10.32Extracting : asn1crypto-1.2.0-py37_0.tar.bz2:  69%|▋| 24/35 [00:02&lt;00:01, 10.32iExtracting : openssl-1.1.1d-h7b6447c_3.tar.bz2:  71%|▋| 25/35 [00:03&lt;00:00, 10.3Extracting : openssl-1.1.1d-h7b6447c_3.tar.bz2:  74%|▋| 26/35 [00:03&lt;00:01,  6.9Extracting : cffi-1.13.0-py37h2e261b9_0.tar.bz2:  74%|▋| 26/35 [00:03&lt;00:01,  6.Extracting : pip-19.3.1-py37_0.tar.bz2:  77%|██▎| 27/35 [00:03&lt;00:01,  6.99it/s]Extracting : pysocks-1.7.1-py37_0.tar.bz2:  80%|▊| 28/35 [00:03&lt;00:01,  5.79it/sExtracting : setuptools-41.4.0-py37_0.tar.bz2:  83%|▊| 29/35 [00:03&lt;00:01,  5.79Extracting : setuptools-41.4.0-py37_0.tar.bz2:  86%|▊| 30/35 [00:03&lt;00:00,  6.82Extracting : ca-certificates-2019.10.16-0.tar.bz2:  86%|▊| 30/35 [00:03&lt;00:00,  Extracting : conda-4.7.12-py37_0.tar.bz2:  89%|▉| 31/35 [00:04&lt;00:00,  6.82it/s]Extracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2:  94%|▉| 33/35 [00:04&lt;00:00Extracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2:  97%|▉| 34/35 [00:04&lt;00:00Extracting : sqlite-3.30.0-h7b6447c_0.tar.bz2:  97%|▉| 34/35 [00:04&lt;00:00,  5.94Extracting : sqlite-3.30.0-h7b6447c_0.tar.bz2: 100%|█| 35/35 [00:04&lt;00:00,  4.70                                                                                Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/zmzforever/sct_dev/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.2.0=py37_0
    - ca-certificates==2019.10.16=0
    - certifi==2019.9.11=py37_0
    - cffi==1.13.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.7.12=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.1=he6710b0_1
    - openssl==1.1.1d=h7b6447c_3
    - pip==19.3.1=py37_0
    - pycosat==0.6.3=py37h14c3975_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.0.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.4=h265db76_1
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_0
    - ruamel_yaml==0.15.46=py37h14c3975_0
    - setuptools==41.4.0=py37_0
    - six==1.12.0=py37_0
    - sqlite==3.30.0=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.36.1=py_0
    - urllib3==1.24.2=py37_0
    - wheel==0.33.6=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cffi               pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.7.12-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  six                pkgs/main/linux-64::six-1.12.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Preparing transaction: done
Executing transaction: done
installation finished.
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/zmzforever/sct_dev/python/envs/venv_sct

  added / updated specs:
    - python=3.6

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2019.9.11          |           py36_0         154 KB
    pip-19.3.1                 |           py36_0         1.9 MB
    python-3.6.9               |       h265db76_0        30.2 MB
    setuptools-42.0.1          |           py36_0         644 KB
    sqlite-3.30.1              |       h7b6447c_0         1.9 MB
    wheel-0.33.6               |           py36_0          40 KB
    ------------------------------------------------------------
                                           Total:        34.9 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py36_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py36_0
  python             pkgs/main/linux-64::python-3.6.9-h265db76_0
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-42.0.1-py36_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.1-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py36_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Proceed ([y]/n)? 

Downloading and Extracting Packages
setuptools-42.0.1    | 644 KB    | ##################################### | 100% 
certifi-2019.9.11    | 154 KB    | ##################################### | 100% 
pip-19.3.1           | 1.9 MB    | ##################################### | 100% 
wheel-0.33.6         | 40 KB     | ##################################### | 100% 
python-3.6.9         | 30.2 MB   | ##################################### | 100% 
sqlite-3.30.1        | 1.9 MB    | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Installing Python dependencies...

Collecting numpy
  Downloading https://files.pythonhosted.org/packages/d2/ab/43e678759326f728de861edbef34b8e2ad1b1490505f20e0d1f0716c3bf4/numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl (20.0MB)
     |████████████████████████████████| 20.0MB 797kB/s 
Installing collected packages: numpy
Successfully installed numpy-1.17.4
Ignoring tensorflow: markers 'platform_system == "Darwin" and "15." in platform_release' don't match your environment
Requirement already satisfied: numpy in ./python/envs/venv_sct/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.17.4)
Collecting cryptography
  Downloading https://files.pythonhosted.org/packages/ca/9a/7cece52c46546e214e10811b36b2da52ce1ea7fa203203a629b8dfadad53/cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl (2.3MB)
     |████████████████████████████████| 2.3MB 570kB/s 
Collecting dipy
  Downloading https://files.pythonhosted.org/packages/5c/c1/fbb9b631cb2de6ff21967069144c00f7d06f522a7098f48a04d7f3b46198/dipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl (8.1MB)
     |████████████████████████████████| 8.1MB 629kB/s 
Collecting futures
  Downloading https://files.pythonhosted.org/packages/05/80/f41cca0ea1ff69bce7e7a7d76182b47bb4e1a494380a532af3e8ee70b9ec/futures-3.1.1-py3-none-any.whl
Collecting h5py
  Downloading https://files.pythonhosted.org/packages/60/06/cafdd44889200e5438b897388f3075b52a8ef01f28a17366d91de0fa2d05/h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl (2.9MB)
     |████████████████████████████████| 2.9MB 591kB/s 
Collecting Keras
  Downloading https://files.pythonhosted.org/packages/ad/fd/6bfe87920d7f4fd475acd28500a42482b6b84479832bdc0fe9e589a60ceb/Keras-2.3.1-py2.py3-none-any.whl (377kB)
     |████████████████████████████████| 378kB 35.3MB/s 
Collecting matplotlib
  Downloading https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl (13.1MB)
     |████████████████████████████████| 13.1MB 818kB/s 
Collecting nibabel
  Downloading https://files.pythonhosted.org/packages/01/13/392132019093ddb7bc997f7f9843d406dc3302a27f01827d2fd028e03c50/nibabel-2.5.1-py3-none-any.whl (3.3MB)
     |████████████████████████████████| 3.3MB 581kB/s 
Collecting pandas
  Downloading https://files.pythonhosted.org/packages/52/3f/f6a428599e0d4497e1595030965b5ba455fd8ade6e977e3c819973c4b41d/pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl (10.4MB)
     |████████████████████████████████| 10.4MB 649kB/s 
Collecting psutil
  Downloading https://files.pythonhosted.org/packages/73/93/4f8213fbe66fc20cb904f35e6e04e20b47b85bee39845cc66a0bcf5ccdcb/psutil-5.6.7.tar.gz (448kB)
     |████████████████████████████████| 450kB 38.6MB/s 
Collecting pyqt5==5.11.3
  Downloading https://files.pythonhosted.org/packages/d4/bf/d884da8e2f7096d201c891d515eb6813a8e85df5eb6f5e12e867bf1d831c/PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8MB)
     |████████████████████████████████| 117.7MB 1.0MB/s eta 0:00:01ERROR: Exception:
Traceback (most recent call last):
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 153, in _main
    status = self.run(options, args)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 382, in run
    resolver.resolve(requirement_set)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 201, in resolve
    self._resolve_one(requirement_set, req)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 365, in _resolve_one
    abstract_dist = self._get_abstract_dist_for(req_to_install)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 313, in _get_abstract_dist_for
    req, self.session, self.finder, self.require_hashes
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 194, in prepare_linked_requirement
    progress_bar=self.progress_bar
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 465, in unpack_url
    progress_bar=progress_bar
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 316, in unpack_http_url
    progress_bar)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 551, in _download_http_url
    _download_url(resp, link, content_file, hashes, progress_bar)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 253, in _download_url
    hashes.check_against_chunks(downloaded_chunks)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/utils/hashes.py", line 80, in check_against_chunks
    for chunk in chunks:
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 223, in written_chunks
    for chunk in chunks:
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/utils/ui.py", line 160, in iter
    for x in it:
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 212, in resp_read
    decode_content=False):
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/urllib3/response.py", line 564, in stream
    data = self.read(amt=amt, decode_content=decode_content)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/urllib3/response.py", line 507, in read
    data = self._fp.read(amt) if not fp_closed else b""
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 65, in read
    self._close()
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 52, in _close
    self.__callback(self.__buf.getvalue())
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/controller.py", line 300, in cache_response
    cache_url, self.serializer.dumps(request, response, body=body)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/serialize.py", line 72, in dumps
    return b",".join([b"cc=4", msgpack.dumps(data, use_bin_type=True)])
MemoryError

Failed running pip install -r requirements.txt: 0

Installation failed

zmzforever@VM-0-14-ubuntu:~/Downloads/spinalcordtoolbox-master$ ./install_sct

*******************************
* Welcome to SCT installation *
*******************************

Checking requirements...

SCT version ......... dev
Installation type ... package
Operating system .... linux
Shell config ........ /home/zmzforever/.bashrc

To improve user experience and fix bugs, the SCT development team is using a
report system to automatically receive crash reports and errors from users.
These reports are anonymous.

Do you agree to help us improve SCT? [y]es/[n]o: y

--&gt; Crash reports will be sent to the SCT development team. Thank you!

SCT will be installed here: [/home/zmzforever/sct_dev]

Do you agree? [y]es/[n]o: y

Copying source files from /home/zmzforever/Downloads/spinalcordtoolbox-master to /home/zmzforever/sct_dev

..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Installing conda...

zmzforever · December 2, 2019, 9:06am

rm -rf /home/zmzforever/sct_dev/python

mkdir -p /home/zmzforever/sct_dev/python

wget -O /tmp/tmp.GxOAKx1HAc/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

--2019-12-02 16:58:42--  https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving repo.continuum.io (repo.continuum.io)... 104.18.200.79, 104.18.201.79, 2606:4700::6812:c94f, ...
Connecting to repo.continuum.io (repo.continuum.io)|104.18.200.79|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 71785000 (68M) [application/x-sh]
Saving to: ‘/tmp/tmp.GxOAKx1HAc/miniconda.sh’

/tmp/tmp.GxOAKx1HAc 100%[===================&gt;]  68.46M  6.84MB/s    in 11s     

2019-12-02 16:58:55 (6.32 MB/s) - ‘/tmp/tmp.GxOAKx1HAc/miniconda.sh’ saved [71785000/71785000]

exit status is 0

bash /tmp/tmp.GxOAKx1HAc/miniconda.sh -p /home/zmzforever/sct_dev/python -b -f

PREFIX=/home/zmzforever/sct_dev/python
Unpacking payload ...
Extracting : libedit-3.1.20181209-hc058e9b_0.conda:   3%| | 1/35 [00:00&lt;00:03,  Extracting : libgcc-ng-9.1.0-hdf63c60_0.conda:   6%| | 2/35 [00:00&lt;00:03,  9.42iExtracting : libgcc-ng-9.1.0-hdf63c60_0.conda:   9%| | 3/35 [00:00&lt;00:03,  8.19iExtracting : urllib3-1.24.2-py37_0.conda:   9%|▏ | 3/35 [00:00&lt;00:03,  8.19it/s]Extracting : pyopenssl-19.0.0-py37_0.conda:  11%| | 4/35 [00:00&lt;00:03,  8.19it/sExtracting : six-1.12.0-py37_0.conda:  14%|▊     | 5/35 [00:00&lt;00:03,  8.19it/s]Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  20%|▏| 7/35 [00:00&lt;00:03,  8.Extracting : libstdcxx-ng-9.1.0-hdf63c60_0.conda:  23%|▏| 8/35 [00:00&lt;00:02, 10.Extracting : python-3.7.4-h265db76_1.conda:  23%|▏| 8/35 [00:01&lt;00:02, 10.52it/sExtracting : libffi-3.2.1-hd88cf55_4.conda:  26%|▎| 9/35 [00:01&lt;00:02, 10.52it/sExtracting : libffi-3.2.1-hd88cf55_4.conda:  29%|▎| 10/35 [00:01&lt;00:05,  4.36it/Extracting : pycparser-2.19-py37_0.conda:  29%|▎| 10/35 [00:01&lt;00:05,  4.36it/s]Extracting : chardet-3.0.4-py37_1003.conda:  31%|▎| 11/35 [00:01&lt;00:05,  4.36it/Extracting : readline-7.0-h7b6447c_5.conda:  34%|▎| 12/35 [00:01&lt;00:05,  4.36it/Extracting : yaml-0.1.7-had09818_2.conda:  37%|▎| 13/35 [00:01&lt;00:05,  4.36it/s]Extracting : conda-package-handling-1.6.0-py37h7b6447c_0.conda:  40%|▍| 14/35 [0Extracting : conda-package-handling-1.6.0-py37h7b6447c_0.conda:  43%|▍| 15/35 [0Extracting : pycosat-0.6.3-py37h14c3975_0.conda:  43%|▍| 15/35 [00:01&lt;00:03,  5.Extracting : tk-8.6.8-hbc83047_0.conda:  46%|█▎ | 16/35 [00:01&lt;00:03,  5.90it/s]Extracting : _libgcc_mutex-0.1-main.conda:  49%|▍| 17/35 [00:01&lt;00:02,  7.10it/sExtracting : ncurses-6.1-he6710b0_1.conda:  51%|▌| 18/35 [00:02&lt;00:02,  7.10it/sExtracting : ncurses-6.1-he6710b0_1.conda:  54%|▌| 19/35 [00:02&lt;00:01,  8.13it/sExtracting : xz-5.2.4-h14c3975_4.conda:  54%|█▋ | 19/35 [00:02&lt;00:01,  8.13it/s]Extracting : ruamel_yaml-0.15.46-py37h14c3975_0.conda:  57%|▌| 20/35 [00:02&lt;00:0Extracting : tqdm-4.36.1-py_0.conda:  60%|███▌  | 21/35 [00:02&lt;00:01,  8.13it/s]Extracting : certifi-2019.9.11-py37_0.tar.bz2:  66%|▋| 23/35 [00:02&lt;00:01, 10.37Extracting : asn1crypto-1.2.0-py37_0.tar.bz2:  69%|▋| 24/35 [00:02&lt;00:01, 10.37iExtracting : asn1crypto-1.2.0-py37_0.tar.bz2:  71%|▋| 25/35 [00:02&lt;00:00, 12.36iExtracting : openssl-1.1.1d-h7b6447c_3.tar.bz2:  71%|▋| 25/35 [00:03&lt;00:00, 12.3Extracting : cffi-1.13.0-py37h2e261b9_0.tar.bz2:  74%|▋| 26/35 [00:03&lt;00:00, 12.Extracting : cffi-1.13.0-py37h2e261b9_0.tar.bz2:  77%|▊| 27/35 [00:03&lt;00:01,  5.Extracting : pip-19.3.1-py37_0.tar.bz2:  77%|██▎| 27/35 [00:03&lt;00:01,  5.79it/s]Extracting : pysocks-1.7.1-py37_0.tar.bz2:  80%|▊| 28/35 [00:03&lt;00:01,  5.79it/sExtracting : pysocks-1.7.1-py37_0.tar.bz2:  83%|▊| 29/35 [00:03&lt;00:01,  5.57it/sExtracting : setuptools-41.4.0-py37_0.tar.bz2:  83%|▊| 29/35 [00:03&lt;00:01,  5.57Extracting : ca-certificates-2019.10.16-0.tar.bz2:  86%|▊| 30/35 [00:03&lt;00:00,  Extracting : ca-certificates-2019.10.16-0.tar.bz2:  89%|▉| 31/35 [00:03&lt;00:00,  Extracting : conda-4.7.12-py37_0.tar.bz2:  89%|▉| 31/35 [00:04&lt;00:00,  6.70it/s]Extracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2:  94%|▉| 33/35 [00:04&lt;00:00Extracting : cryptography-2.8-py37h1ba5d50_0.tar.bz2:  97%|▉| 34/35 [00:04&lt;00:00Extracting : sqlite-3.30.0-h7b6447c_0.tar.bz2:  97%|▉| 34/35 [00:04&lt;00:00,  5.24Extracting : sqlite-3.30.0-h7b6447c_0.tar.bz2: 100%|█| 35/35 [00:04&lt;00:00,  4.47                                                                                Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/zmzforever/sct_dev/python

  added / updated specs:
    - _libgcc_mutex==0.1=main
    - asn1crypto==1.2.0=py37_0
    - ca-certificates==2019.10.16=0
    - certifi==2019.9.11=py37_0
    - cffi==1.13.0=py37h2e261b9_0
    - chardet==3.0.4=py37_1003
    - conda-package-handling==1.6.0=py37h7b6447c_0
    - conda==4.7.12=py37_0
    - cryptography==2.8=py37h1ba5d50_0
    - idna==2.8=py37_0
    - libedit==3.1.20181209=hc058e9b_0
    - libffi==3.2.1=hd88cf55_4
    - libgcc-ng==9.1.0=hdf63c60_0
    - libstdcxx-ng==9.1.0=hdf63c60_0
    - ncurses==6.1=he6710b0_1
    - openssl==1.1.1d=h7b6447c_3
    - pip==19.3.1=py37_0
    - pycosat==0.6.3=py37h14c3975_0
    - pycparser==2.19=py37_0
    - pyopenssl==19.0.0=py37_0
    - pysocks==1.7.1=py37_0
    - python==3.7.4=h265db76_1
    - readline==7.0=h7b6447c_5
    - requests==2.22.0=py37_0
    - ruamel_yaml==0.15.46=py37h14c3975_0
    - setuptools==41.4.0=py37_0
    - six==1.12.0=py37_0
    - sqlite==3.30.0=h7b6447c_0
    - tk==8.6.8=hbc83047_0
    - tqdm==4.36.1=py_0
    - urllib3==1.24.2=py37_0
    - wheel==0.33.6=py37_0
    - xz==5.2.4=h14c3975_4
    - yaml==0.1.7=had09818_2
    - zlib==1.2.11=h7b6447c_3

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  asn1crypto         pkgs/main/linux-64::asn1crypto-1.2.0-py37_0
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py37_0
  cffi               pkgs/main/linux-64::cffi-1.13.0-py37h2e261b9_0
  chardet            pkgs/main/linux-64::chardet-3.0.4-py37_1003
  conda              pkgs/main/linux-64::conda-4.7.12-py37_0
  conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
  cryptography       pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
  idna               pkgs/main/linux-64::idna-2.8-py37_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py37_0
  pycosat            pkgs/main/linux-64::pycosat-0.6.3-py37h14c3975_0
  pycparser          pkgs/main/linux-64::pycparser-2.19-py37_0
  pyopenssl          pkgs/main/linux-64::pyopenssl-19.0.0-py37_0
  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py37_0
  python             pkgs/main/linux-64::python-3.7.4-h265db76_1
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  requests           pkgs/main/linux-64::requests-2.22.0-py37_0
  ruamel_yaml        pkgs/main/linux-64::ruamel_yaml-0.15.46-py37h14c3975_0
  setuptools         pkgs/main/linux-64::setuptools-41.4.0-py37_0
  six                pkgs/main/linux-64::six-1.12.0-py37_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.0-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  tqdm               pkgs/main/noarch::tqdm-4.36.1-py_0
  urllib3            pkgs/main/linux-64::urllib3-1.24.2-py37_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py37_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  yaml               pkgs/main/linux-64::yaml-0.1.7-had09818_2
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Preparing transaction: done
Executing transaction: done
installation finished.
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/zmzforever/sct_dev/python/envs/venv_sct

  added / updated specs:
    - python=3.6

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2019.9.11          |           py36_0         154 KB
    pip-19.3.1                 |           py36_0         1.9 MB
    python-3.6.9               |       h265db76_0        30.2 MB
    setuptools-42.0.1          |           py36_0         644 KB
    sqlite-3.30.1              |       h7b6447c_0         1.9 MB
    wheel-0.33.6               |           py36_0          40 KB
    ------------------------------------------------------------
                                           Total:        34.9 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  ca-certificates    pkgs/main/linux-64::ca-certificates-2019.10.16-0
  certifi            pkgs/main/linux-64::certifi-2019.9.11-py36_0
  libedit            pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0
  libffi             pkgs/main/linux-64::libffi-3.2.1-hd88cf55_4
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            pkgs/main/linux-64::ncurses-6.1-he6710b0_1
  openssl            pkgs/main/linux-64::openssl-1.1.1d-h7b6447c_3
  pip                pkgs/main/linux-64::pip-19.3.1-py36_0
  python             pkgs/main/linux-64::python-3.6.9-h265db76_0
  readline           pkgs/main/linux-64::readline-7.0-h7b6447c_5
  setuptools         pkgs/main/linux-64::setuptools-42.0.1-py36_0
  sqlite             pkgs/main/linux-64::sqlite-3.30.1-h7b6447c_0
  tk                 pkgs/main/linux-64::tk-8.6.8-hbc83047_0
  wheel              pkgs/main/linux-64::wheel-0.33.6-py36_0
  xz                 pkgs/main/linux-64::xz-5.2.4-h14c3975_4
  zlib               pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3

Proceed ([y]/n)? 

Downloading and Extracting Packages
certifi-2019.9.11    | 154 KB    | ##################################### | 100% 
wheel-0.33.6         | 40 KB     | ##################################### | 100% 
setuptools-42.0.1    | 644 KB    | ##################################### | 100% 
pip-19.3.1           | 1.9 MB    | ##################################### | 100% 
python-3.6.9         | 30.2 MB   | ##################################### | 100% 
sqlite-3.30.1        | 1.9 MB    | ##################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate venv_sct
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Installing Python dependencies...

Collecting numpy
  Using cached https://files.pythonhosted.org/packages/d2/ab/43e678759326f728de861edbef34b8e2ad1b1490505f20e0d1f0716c3bf4/numpy-1.17.4-cp36-cp36m-manylinux1_x86_64.whl
Installing collected packages: numpy
Successfully installed numpy-1.17.4
Ignoring tensorflow: markers 'platform_system == "Darwin" and "15." in platform_release' don't match your environment
Requirement already satisfied: numpy in ./python/envs/venv_sct/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.17.4)
Collecting cryptography
  Using cached https://files.pythonhosted.org/packages/ca/9a/7cece52c46546e214e10811b36b2da52ce1ea7fa203203a629b8dfadad53/cryptography-2.8-cp34-abi3-manylinux2010_x86_64.whl
Collecting dipy
  Using cached https://files.pythonhosted.org/packages/5c/c1/fbb9b631cb2de6ff21967069144c00f7d06f522a7098f48a04d7f3b46198/dipy-1.0.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting futures
  Using cached https://files.pythonhosted.org/packages/05/80/f41cca0ea1ff69bce7e7a7d76182b47bb4e1a494380a532af3e8ee70b9ec/futures-3.1.1-py3-none-any.whl
Collecting h5py
  Using cached https://files.pythonhosted.org/packages/60/06/cafdd44889200e5438b897388f3075b52a8ef01f28a17366d91de0fa2d05/h5py-2.10.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting Keras
  Using cached https://files.pythonhosted.org/packages/ad/fd/6bfe87920d7f4fd475acd28500a42482b6b84479832bdc0fe9e589a60ceb/Keras-2.3.1-py2.py3-none-any.whl
Collecting matplotlib
  Using cached https://files.pythonhosted.org/packages/4e/11/06958a2b895a3853206dea1fb2a5b11bf044f626f90745987612af9c8f2c/matplotlib-3.1.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting nibabel
  Using cached https://files.pythonhosted.org/packages/01/13/392132019093ddb7bc997f7f9843d406dc3302a27f01827d2fd028e03c50/nibabel-2.5.1-py3-none-any.whl

Collecting pandas
  Using cached https://files.pythonhosted.org/packages/52/3f/f6a428599e0d4497e1595030965b5ba455fd8ade6e977e3c819973c4b41d/pandas-0.25.3-cp36-cp36m-manylinux1_x86_64.whl
Collecting psutil
  Using cached https://files.pythonhosted.org/packages/73/93/4f8213fbe66fc20cb904f35e6e04e20b47b85bee39845cc66a0bcf5ccdcb/psutil-5.6.7.tar.gz
Collecting pyqt5==5.11.3
  Downloading https://files.pythonhosted.org/packages/d4/bf/d884da8e2f7096d201c891d515eb6813a8e85df5eb6f5e12e867bf1d831c/PyQt5-5.11.3-5.11.2-cp35.cp36.cp37.cp38-abi3-manylinux1_x86_64.whl (117.8MB)
     |████████████████████████████████| 117.7MB 517kB/s eta 0:00:01ERROR: Exception:
Traceback (most recent call last):
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/cli/base_command.py", line 153, in _main
    status = self.run(options, args)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/commands/install.py", line 382, in run
    resolver.resolve(requirement_set)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 201, in resolve
    self._resolve_one(requirement_set, req)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 365, in _resolve_one
    abstract_dist = self._get_abstract_dist_for(req_to_install)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/legacy_resolve.py", line 313, in _get_abstract_dist_for
    req, self.session, self.finder, self.require_hashes
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/operations/prepare.py", line 194, in prepare_linked_requirement
    progress_bar=self.progress_bar
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 465, in unpack_url
    progress_bar=progress_bar
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 316, in unpack_http_url
    progress_bar)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 551, in _download_http_url
    _download_url(resp, link, content_file, hashes, progress_bar)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 253, in _download_url
    hashes.check_against_chunks(downloaded_chunks)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/utils/hashes.py", line 80, in check_against_chunks
    for chunk in chunks:
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 223, in written_chunks
    for chunk in chunks:
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/utils/ui.py", line 160, in iter
    for x in it:
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_internal/download.py", line 212, in resp_read
    decode_content=False):
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/urllib3/response.py", line 564, in stream
    data = self.read(amt=amt, decode_content=decode_content)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/urllib3/response.py", line 507, in read
    data = self._fp.read(amt) if not fp_closed else b""
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 65, in read
    self._close()
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/filewrapper.py", line 52, in _close
    self.__callback(self.__buf.getvalue())
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/controller.py", line 300, in cache_response
    cache_url, self.serializer.dumps(request, response, body=body)
  File "/home/zmzforever/sct_dev/python/envs/venv_sct/lib/python3.6/site-packages/pip/_vendor/cachecontrol/serialize.py", line 72, in dumps
    return b",".join([b"cc=4", msgpack.dumps(data, use_bin_type=True)])
MemoryError

Failed running pip install -r requirements.txt: 0

Installation failed

zmzforever@VM-0-14-ubuntu:~/Downloads/spinalcordtoolbox-master$

jcohenadad · December 2, 2019, 3:40pm

@zmzforever there is a MemoryError. Could you try to allocate more RAM on your VM? How much total RAM do you have on your machine? How much did you allocate to your VM?

jcohenadad · December 2, 2019, 4:30pm

@zmzforever for info: we were able to reproduce your error (see here). While we work on a fix, you should be able to use SCT, except for the GUI part. If you need the GUI, you could replace the manual interventions with a third-party viewer such as FSLeyes.

jcohenadad · December 2, 2019, 6:23pm

@zmzforever we found a fix for your issue (thank you @alexandrufoias). Solution is described here.

zmzforever · December 3, 2019, 3:00am

Try to insert Guest Additions CD image:

Could not mount the media/drive ‘C:\Program Files\Oracle\VirtualBox/VBoxGuestAdditions.iso’ (VERR_PDM_MEDIA_LOCKED).

E_FAIL (0x80004005)
ConsoleWrap
IConsole {872da645-4a9b-1727-bee2-5585105b9eed}
: IMachine {5047460a-265d-4538-b23e-ddba5fb84976}

Cannot see the icon. So I google my question and run:

brain@neurodebian:~$ su root
Password:
root@neurodebian:/home/brain# mkdir /media/cdrom
mkdir: cannot create directory `/media/cdrom’: File exists
root@neurodebian:/home/brain# mount /dev/sr0 /media/cdrom
mount: no medium found on /dev/sr0
root@neurodebian:/home/brain# ./VBoxLinuxAdditions.run
bash: ./VBoxLinuxAdditions.run: No such file or directory
root@neurodebian:/home/brain# sudo umount /media/title-of-cd
umount: /media/title-of-cd: not found

jcohenadad · December 3, 2019, 3:16pm

@zmzforever we are looking into a solution.

In the meantime, could you please let us know what specifically didn’t work when you tried to install SCT via Docker? That approach could also be viable alternative for you.

zmzforever · December 4, 2019, 1:16am

It was nearly 2 weeks ago, so I couldn’t remember details. I installed Docker and followed the protocols.
At the beginning, I got wrong when I needed to find share folders. I tried to fix it through the alternative steps, but it didn’t work. So I updated my windows, uninstalled and reinstalled Docker for several times. Though I didn’t see new folders in C/users/docker_folder_shared, I managed to run SCT on Docker. However, it just shut down. It reminded me there was no enough room for containers, so I googled it and saw various possible solutions:

docker-win “Not enough memory to start Docker” #1021

Not enough memory to start Docker #956

I am using my laptop. I guess it has some relationship with this. So I turned to VBox and VM, installed Neurodebian and ran SCT successfully, It worked at first, but I wanted to copy folders between VBox and My computer, so I inserted GeustAddition. Suddenly my mouse couldn’t move:

You have clicked the mouse inside the Virtual Machine display or pressed the…

I uninstalled and reinstalled VBox and Neurodebian again for several times. Now I am here. Neurodebian is installed. Cannot use SCT.

jcohenadad · December 4, 2019, 1:52am

@zmzforever can you try this fix for installing guest addition CD?